Supervisors: Melody Clark (British Antarctic Survey), Bill Amos (Zoology), Pietro Lio (Computer Laboratory) and Lloyd Peck (British Antarctic Survey)
Importance of the area of research:
Understanding species’ responses to environmental change underpins our abilities to predict future biodiversity and the state of ecosystems under any range of scenarios. This is particularly important in global regions undergoing rapid warming, with fragile ecosystems, such as the poles. Detailed evaluations are best achieved at the molecular level, by understanding which biochemical pathways are most affected by changing conditions and then evaluating impacts on whole animal resilience or sensitivity (Clark et al., 2016). This proposal, using a multiple species approach (the sea urchin Sterechinus neumayeri, the limpet Nacella concinna and the crustacean Paraceradocus meirsii as a minimum, tested across 4 temperature regimes, including a 3 month acclimation) with extensive ecological metadata on the chosen species (Peck et al., 2009), will enable predictive, mechanistic evaluations of responses to climate change from cellular to macroscopic scales, including ecosystems' and global scales. The aim is for the analyses to take recent the contributions of theoretical computer science to life sciences, drawing on biophysics and biomathematics to develop predictive scenarios for Antarctic ecosystems under threat (cf. Angione et al., 2016).
This project will characterise underlying cellular mechanisms of responses to warming in Antarctic marine species and use these as proxies for predicting ecosystem resilience using modelling approaches. We will use transcriptomic data to test the hypothesis that the current overarching paradigms on sensitivity to changing conditions (e.g. oxygen limitation, conserved stress response, accumulation of toxic oxidised proteins etc.) do not universally apply across species and stressors. We propose that responses to change are species and context-specific, that this approach allows us to identify biochemical pinch-points in each species, and population level variability of these genes impacts levels of phenotypic plasticity.
What the student will do:
We already have Illumina 2000 150bp paired end read sequence data from thermal ramping experiments on three Antarctic marine invertebrates with different known thermal resiliences, warmed at 1°C h-1, 1°C dy-1, 1°C/3 days and 2 months acclimation at 2°C (Peck et al., 2009). This is a unique dataset, with all species treated identically. The student will assemble, map and annotate all the reads for each species. Expression profiles will be used in gene network and multi-layered network analyses (Angione et al. 2016) to identify underlying cellular responses to warming treatments and predict long term responses. We will also adapt static analysis, module identification and decomposition, model reductions and model inference methods to provide further detail on particular pathways identified. A core gene set, identified via computational approaches, will be further examined using multiplex PCR and SNP analysis to examine variability within wider populations to evaluate phenotypic plasticity to changing environments.
Please contact the lead supervisor directly for further information relating to what the successful applicant will be expected to do, training to be provided, and any specific educational background requirements.
Clark, M.S., Sommer, U., Sihra, J.K., Thorne, M.A.S., Morley, S.A., King, M., Viant, M.R., Peck, L.S. (2016) Biodiversity in marine invertebrate responses to acute warming revealed by a comparative multi-omics approach. Global Change Biology DOI: 10.1111/gcb.13357
Angione, C., Conway, M. & Lio’, P. (2016) Multiplex models provide effective integration of multiomic data in genome scale models. BMC Bioinformatics, vol. 17, pp.257. DOI: 10.1186/s12859-016-0912-1
Peck, L.S., Clark, M.S., Morley, S.A., Massey, A., Rosetti, H (2009) Animal temperature limits: effects of size, activity and rates of change. Functional Ecology, vol. 23, pp.248-256. DOI: 10.1111/j.1365-2435.2008.01537.x